R interface to genome browsers and their annotation tracks


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Documentation for package ‘rtracklayer’ version 1.6.0

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A B C E G I N R S T U V misc

-- --

$,BrowserSession-method Class "BrowserSession"
$<-,BrowserSession,ANY,RangedDataORRangedDataList-method Class "BrowserSession"

-- A --

activeView Accessing the active view
activeView,BrowserSession-method Accessing the active view
activeView,UCSCView-method Accessing the active view
activeView-methods Accessing the active view
activeView<- Accessing the active view
activeView<--methods Accessing the active view

-- B --

BasicTrackLine-class Class "BasicTrackLine"
Bed15TrackLine-class Class "Bed15TrackLine"
blocks Get blocks/exons
blocks,RangedData-method Get blocks/exons
blocks-methods Get blocks/exons
browseGenome Browse a genome
browseGenome,missing-method Browse a genome
browseGenome,RangedDataORRangedDataList-method Browse a genome
browserSession Get a genome browser session
browserSession,BrowserView-method Get a genome browser session
browserSession,character-method Get a genome browser session
browserSession,missing-method Get a genome browser session
browserSession,UCSCTableQuery-method Querying UCSC Tables
BrowserSession-class Class "BrowserSession"
browserSession-methods Get a genome browser session
browserSession<- Querying UCSC Tables
browserSession<-,UCSCTableQuery,UCSCSession-method Querying UCSC Tables
browserView Getting browser views
browserView,UCSCSession-method Getting browser views
BrowserView-class Class "BrowserView"
browserView-methods Getting browser views
browserViews Getting the browser views
browserViews,UCSCSession-method Getting the browser views
browserViews-methods Getting the browser views

-- C --

chrom Data on a Genome
chrom,RangedData-method Data on a Genome
chrom,RangesList-method Ranges on a Genome
chrom<- Data on a Genome
chrom<-,RangedData-method Data on a Genome
chrom<-,RangesList-method Ranges on a Genome
coerce,BasicTrackLine,character-method Class "BasicTrackLine"
coerce,BasicTrackLine,GraphTrackLine-method Class "GraphTrackLine"
coerce,Bed15TrackLine,character-method Class "Bed15TrackLine"
coerce,character,BasicTrackLine-method Class "BasicTrackLine"
coerce,character,Bed15TrackLine-method Class "Bed15TrackLine"
coerce,character,GraphTrackLine-method Class "GraphTrackLine"
coerce,character,TrackLine-method Class "TrackLine"
coerce,GraphTrackLine,BasicTrackLine-method Class "GraphTrackLine"
coerce,GraphTrackLine,character-method Class "GraphTrackLine"
coerce,RangedData,UCSCData-method Class "UCSCData"
coerce,TrackLine,character-method Class "TrackLine"
cpneTrack CPNE1 SNP track

-- E --

export Export objects to connections
export,ANY,character,character-method Export objects to connections
export,ANY,character,missing-method Export objects to connections
export,ANY,connection,character-method Export objects to connections
export,ANY,missing,character-method Export objects to connections
export.bed Export tracks
export.bed,ANY,ANY-method Export tracks
export.bed,RangedData,characterORconnection-method Export tracks
export.bed,RangedDataList,ANY-method Export tracks
export.bed,UCSCData,ANY-method Class "UCSCData"
export.bed15 Export tracks
export.bed15,ANY-method Export tracks
export.bed15,UCSCData-method Class "UCSCData"
export.bedGraph Export tracks
export.bedGraph,ANY-method Export tracks
export.gff Export tracks
export.gff,ANY,ANY-method Export tracks
export.gff,RangedData,characterORconnection-method Export tracks
export.gff,UCSCData,characterORconnection-method Class "UCSCData"
export.gff1 Export tracks
export.gff1,ANY-method Export tracks
export.gff2 Export tracks
export.gff2,ANY-method Export tracks
export.gff3 Export tracks
export.gff3,ANY-method Export tracks
export.ucsc Export tracks
export.ucsc,ANY,ANY-method Export tracks
export.ucsc,RangedData,ANY-method Export tracks
export.ucsc,RangedDataList,ANY-method Export tracks
export.ucsc,UCSCData,characterORconnection-method Class "UCSCData"
export.wig Export tracks
export.wig,ANY-method Export tracks

-- G --

genome Data on a Genome
genome,BrowserSession-method Class "BrowserSession"
genome,RangedData-method Data on a Genome
genome,RangesList-method Ranges on a Genome
genome,UCSCSession-method Class "UCSCSession"
genome<- Data on a Genome
genome<-,BrowserSession-method Class "BrowserSession"
genome<-,RangedData-method Data on a Genome
genome<-,RangesList-method Ranges on a Genome
genome<-,UCSCSession-method Class "UCSCSession"
genomeBrowsers Get available genome browsers
GenomicData Data on a Genome
GenomicRanges Ranges on a Genome
getSeq,UCSCSession-method Retrieving a genome sequence
getTable Querying UCSC Tables
getTable,UCSCTableQuery-method Querying UCSC Tables
GraphTrackLine-class Class "GraphTrackLine"

-- I --

import Importing objects
import,character,character,ANY-method Importing objects
import,character,missing,ANY-method Importing objects
import,connection,character,ANY-method Importing objects
import,missing,ANY,character-method Importing objects
import.bed Importing tracks
import.bed,connection-method Importing tracks
import.bed15 Importing tracks
import.bed15,ANY-method Importing tracks
import.bedGraph Importing tracks
import.bedGraph,ANY-method Importing tracks
import.gff Importing tracks
import.gff,characterORconnection-method Importing tracks
import.gff1 Importing tracks
import.gff1,ANY-method Importing tracks
import.gff2 Importing tracks
import.gff2,ANY-method Importing tracks
import.gff3 Importing tracks
import.gff3,ANY-method Importing tracks
import.ucsc Importing tracks
import.ucsc,characterORconnection-method Importing tracks
import.wig Importing tracks
import.wig,ANY-method Importing tracks
initialize,UCSCData-method Class "UCSCData"
initialize,UCSCSession-method Class "UCSCSession"

-- N --

names,UCSCTableQuery-method Querying UCSC Tables
names<-,UCSCTableQuery-method Querying UCSC Tables

-- R --

range,BrowserSession-method Class "BrowserSession"
range,ucscCart-method Class "UCSCSession"
range,UCSCSession-method Class "UCSCSession"
range,UCSCTableQuery-method Querying UCSC Tables
range,UCSCView-method Class "UCSCView"
range<- Class "UCSCSession"
range<-,UCSCSession,RangesList-method Class "UCSCSession"
range<-,UCSCTableQuery,RangesList-method Querying UCSC Tables
range<-,UCSCView,RangesList-method Class "UCSCView"
RangedData-methods Data on a Genome
RangesList-methods Ranges on a Genome

-- S --

sequence<- Load a sequence
sequence<--methods Load a sequence
show,BrowserSession-method Class "BrowserSession"
show,BrowserView-method Class "BrowserView"
show,TrackLine-method Class "TrackLine"
show,UCSCData-method Class "UCSCData"
show,UCSCTableQuery-method Querying UCSC Tables

-- T --

tableName Querying UCSC Tables
tableName,UCSCTableQuery-method Querying UCSC Tables
tableName<- Querying UCSC Tables
tableName<-,UCSCTableQuery-method Querying UCSC Tables
tableNames Querying UCSC Tables
tableNames,UCSCTableQuery-method Querying UCSC Tables
targets microRNA target sites
track Querying UCSC Tables
track,UCSCSession-method Class "UCSCSession"
track,UCSCTableQuery-method Querying UCSC Tables
track<- Laying tracks
track<-,BrowserSession,RangedData-method Laying tracks
track<-,BrowserSession,RangedDataList-method Laying tracks
track<-,UCSCSession,RangedDataList-method Laying tracks
track<--methods Laying tracks
TrackLine-class Class "TrackLine"
trackName Querying UCSC Tables
trackName,UCSCTableQuery-method Querying UCSC Tables
trackName<- Querying UCSC Tables
trackName<-,UCSCTableQuery-method Querying UCSC Tables
trackNames Accessing track names
trackNames,UCSCSession-method Accessing track names
trackNames,UCSCTableQuery-method Querying UCSC Tables
trackNames,UCSCTrackModes-method Accessing track names
trackNames,UCSCView-method Accessing track names
trackNames-methods Accessing track names
trackNames<- Accessing track names
trackNames<-,UCSCTrackModes-method Accessing track names
trackNames<-,UCSCView-method Accessing track names
trackNames<--methods Accessing track names

-- U --

UCSCData-class Class "UCSCData"
ucscGenomes Get available genomes on UCSC
UCSCSession-class Class "UCSCSession"
ucscTableQuery Querying UCSC Tables
ucscTableQuery,UCSCSession-method Querying UCSC Tables
UCSCTableQuery-class Querying UCSC Tables
ucscTrackModes Accessing UCSC track modes
ucscTrackModes,character-method Accessing UCSC track modes
ucscTrackModes,missing-method Accessing UCSC track modes
ucscTrackModes,UCSCSession-method Accessing UCSC track modes
ucscTrackModes,ucscTracks-method Accessing UCSC track modes
ucscTrackModes,UCSCView-method Accessing UCSC track modes
UCSCTrackModes-class Class "UCSCTrackModes"
ucscTrackModes-methods Accessing UCSC track modes
ucscTrackModes<- Accessing UCSC track modes
ucscTrackModes<-,UCSCView,character-method Accessing UCSC track modes
ucscTrackModes<-,UCSCView,UCSCTrackModes-method Accessing UCSC track modes
ucscTrackModes<--methods Accessing UCSC track modes
UCSCView-class Class "UCSCView"

-- V --

visible Class "BrowserView"
visible,BrowserView-method Class "BrowserView"
visible,UCSCView-method Class "UCSCView"
visible<- Class "BrowserView"
visible<-,BrowserView-method Class "BrowserView"
visible<-,UCSCView-method Class "UCSCView"

-- misc --

[,UCSCTrackModes-method Class "UCSCTrackModes"
[<-,UCSCTrackModes-method Class "UCSCTrackModes"
[[,BrowserSession-method Class "BrowserSession"
[[<-,BrowserSession,ANY,ANY,RangedDataORRangedDataList-method Class "BrowserSession"